From 5a9260d39b73b280f3f91fda69b198de02f113bd Mon Sep 17 00:00:00 2001
From: Michael Hartung <michi@Michaels-MacBook-Pro.local>
Date: Wed, 25 Aug 2021 19:06:11 +0200
Subject: [PATCH] load edges from db
---
src/app/config.ts | 2 ++
src/app/interfaces.ts | 5 +++++
src/app/main-network.ts | 17 ++++++++++++++++-
.../explorer-page/explorer-page.component.ts | 13 +++++++++++--
.../netex-controller.service.ts | 11 ++++++++++-
src/index.html | 7 +++----
6 files changed, 47 insertions(+), 8 deletions(-)
diff --git a/src/app/config.ts b/src/app/config.ts
index ead040c5..2abf461d 100644
--- a/src/app/config.ts
+++ b/src/app/config.ts
@@ -56,6 +56,7 @@ export interface IConfig {
edgeGroups: { [key: string]: EdgeGroup };
interactionDrugProtein: InteractionDrugProteinDB;
interactionProteinProtein: InteractionProteinProteinDB;
+ autofillEdges: boolean;
interactions?: InteractionDatabase;
identifier?: Identifier;
nodeShadow?: boolean;
@@ -93,6 +94,7 @@ export const defaultConfig: IConfig = {
interactionProteinProtein: 'STRING',
nodeShadow: true,
edgeShadow: true,
+ autofillEdges: true,
nodeGroups: {
// all NodeGroups but the default group must be set, if not provided by the user, they will be taken from here
// IMPORTANT: node color must be hexacode!
diff --git a/src/app/interfaces.ts b/src/app/interfaces.ts
index cab05e03..2c467aad 100644
--- a/src/app/interfaces.ts
+++ b/src/app/interfaces.ts
@@ -37,6 +37,11 @@ export type legendContext = 'explorer' | 'adjacentDrugs' | 'drug' | 'drugTarget'
/// netexId to expressionlvl
export type NodeAttributeMap = { string: number } | {};
+export interface NetexInteraction {
+ dataset: string;
+ proteinA: string;
+ proteinB: string;
+}
export interface NodeInteraction {
from: string;
diff --git a/src/app/main-network.ts b/src/app/main-network.ts
index 1abe89b4..e2a99291 100644
--- a/src/app/main-network.ts
+++ b/src/app/main-network.ts
@@ -1,5 +1,5 @@
import { defaultConfig, IConfig } from './config';
-import {NodeInteraction, Node, getProteinNodeId} from './interfaces';
+import {NodeInteraction, Node, getProteinNodeId, NetexInteraction} from './interfaces';
import * as merge from 'lodash/fp/merge';
export function getDatasetFilename(dataset: Array<[string, string]>): string {
@@ -117,3 +117,18 @@ export function mapCustomEdge(customEdge: NodeInteraction, config: IConfig): any
};
return edge;
}
+
+/** Maps netex retrieved edge to network edge object
+ * Uses the default group for edge objects.
+ *
+ * @param customEdge
+ * @param config
+ * @returns
+ */
+ export function mapNetexEdge(customEdge: NetexInteraction, config: IConfig): any {
+ const edge = JSON.parse(JSON.stringify(config.edgeGroups.default));
+ edge['from'] = customEdge['proteinA'];
+ edge['to'] = customEdge['proteinB'];
+ edge['dataset'] = customEdge['dataset'];
+ return edge;
+}
diff --git a/src/app/pages/explorer-page/explorer-page.component.ts b/src/app/pages/explorer-page/explorer-page.component.ts
index fa2a95db..7e7c2ef1 100644
--- a/src/app/pages/explorer-page/explorer-page.component.ts
+++ b/src/app/pages/explorer-page/explorer-page.component.ts
@@ -18,7 +18,7 @@ import {
Tissue,
Wrapper
} from '../../interfaces';
-import {mapCustomEdge, mapCustomNode, ProteinNetwork} from '../../main-network';
+import {mapCustomEdge, mapCustomNode, mapNetexEdge, ProteinNetwork} from '../../main-network';
import {AnalysisService} from '../../services/analysis/analysis.service';
import {OmnipathControllerService} from '../../services/omnipath-controller/omnipath-controller.service';
import domtoimage from 'dom-to-image';
@@ -369,10 +369,19 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
if (this.networkPositions) {
this.proteinData.updateNodePositions(this.networkPositions)
}
- this.proteinData.linkNodes();
+ // TODO do we still need this?
+ // this.proteinData.linkNodes();
const {nodes, edges} = this.proteinData.mapDataToNetworkInput(this.myConfig);
+ console.log('nodes', nodes)
+ console.log('edges', edges)
+ if (this.myConfig.autofillEdges && nodes.length) {
+ const netexEdges = await this.netex.fetchEdges(nodes, this.myConfig.interactionProteinProtein);
+ console.log(netexEdges.map(netexEdge => mapNetexEdge(netexEdge, this.myConfig)))
+ edges.push(...netexEdges.map(netexEdge => mapNetexEdge(netexEdge, this.myConfig)))
+ }
+
this.nodeData.nodes = new vis.DataSet(nodes);
this.nodeData.edges = new vis.DataSet(edges);
const container = this.networkEl.nativeElement;
diff --git a/src/app/services/netex-controller/netex-controller.service.ts b/src/app/services/netex-controller/netex-controller.service.ts
index 4992123d..bfc7e285 100644
--- a/src/app/services/netex-controller/netex-controller.service.ts
+++ b/src/app/services/netex-controller/netex-controller.service.ts
@@ -4,7 +4,7 @@ import {HttpClient, HttpParams} from '@angular/common/http';
import {AlgorithmType, QuickAlgorithmType} from '../analysis/analysis.service';
import { Observable } from 'rxjs';
import { Tissue, Node, EdgeType} from 'src/app/interfaces';
-import { InteractionDrugProteinDB } from 'src/app/config';
+import { InteractionDrugProteinDB, InteractionProteinProteinDB } from 'src/app/config';
@Injectable({
providedIn: 'root'
@@ -115,4 +115,13 @@ export class NetexControllerService {
*/
return this.http.post(`${environment.backend}graph_export/`, graph_data, {responseType: 'text'});
}
+
+ public async fetchEdges(nodes: Node[], dataset: InteractionProteinProteinDB): Promise<any> {
+ /**
+ * Tries to map every node to a node object in out database
+ * Returns list of mapped nodes if node was found, otherwise original node to not lose information
+ */
+ const payload = {nodes: nodes, dataset: dataset};
+ return this.http.post(`${environment.backend}fetch_edges/`, payload).toPromise();
+ }
}
diff --git a/src/index.html b/src/index.html
index ea00bbd9..b7e2e5dd 100644
--- a/src/index.html
+++ b/src/index.html
@@ -44,14 +44,13 @@
"identifier": "symbol",
"nodeShadow": true,
"edgeShadow": true,
- "interactionDrugProtein": "ChEMBL",
- "legendUrl": "https://exbio.wzw.tum.de/covex/assets/leg1.png"
+ "interactionProteinProtein": "APID",
+ "interactionDrugProtein": "ChEMBL"
}'
network='{
"nodes": [{"id": "TP53", "group": "0.5"}, {"id": "MYC", "group": "pugGroup"}, {"id": "Patient No. 5", "group": "patientgroup"}, {"label": "PTEN", "id": "PTEN", "group": 0.5, "value":"5"}],
"edges": [
- {"from": "TP53","to": "C5","group": "xxx", "label": "this is a label", "title": "this is a title"},
- {"from": "Patient No. 5","to": "C5","label": "w/o group"}
+
]
}'
style="height: 100%; width: 100vw; display: block;"
--
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